Complete Genome Sequence of Yellow Pigment-Producing Sphingobium sp. Strain HAL-16.
ABSTRACT: Sphingobium sp. strain HAL-16, which was isolated from Antarctic soil samples, synthesizes a yellow pigment. The complete genome consists of a single circular chromosome (4,372,398?bp, with a G+C content of 62.7%) and a single circular plasmid (57,025?bp, with a G+C content of 59.4%). Five genes encoding carotenogenic enzymes were identified, suggesting that the yellow pigment is a hydroxy/keto-?-carotene.
Project description:BACKGROUND: The histidine ammonia-lyse gene (HAL) encodes the histidine ammonia-lyase, which catalyzes the first reaction of histidine catabolism. In our previous genome-wide association study in Chinese Holstein cows to identify genetic variants affecting milk production traits, a SNP (rs41647754) located 357 bp upstream of HAL, was found to be significantly associated with milk yield and milk protein yield. In addition, the HAL gene resides within the reported QTLs for milk production traits. The aims of this study were to identify genetic variants in HAL and to test the association between these variants and milk production traits. RESULTS: Fifteen SNPs were identified within the regions under study of the HAL gene, including three coding mutations, seven intronic mutations, one promoter region mutation, and four 3'UTR mutations. Nine of these identified SNPs were chosen for subsequent genotyping and association analyses. Our results showed that five SNP markers (ss974768522, ss974768525, ss974768531, ss974768533 and ss974768534) were significantly associated with one or more milk production traits. Haplotype analysis showed that two haplotype blocks were significantly associated with milk yield and milk protein yield, providing additional support for the association between HAL variants and milk production traits in dairy cows (P < 0.05). CONCLUSION: Our study shows evidence of significant associations between SNPs within the HAL gene and milk production traits in Chinese Holstein cows, indicating the potential role of HAL variants in these traits. These identified SNPs may serve as genetic markers used in genomic selection schemes to accelerate the genetic gains of milk production traits in dairy cattle.
Project description:<h4>Introduction</h4>The Haemophilia Activities List (HAL) was developed to measure activities and participation in persons with haemophilia (PWH). Shortening the questionnaire may facilitate use of the HAL.<h4>Aim</h4>The aim of this study was to determine which items of the HAL are redundant, to construct a shorter version of the HAL, and to determine the construct validity of the HAL<sub>short</sub> .<h4>Methods</h4>A secondary analysis was performed on pooled data of two published studies using the HAL (seven domains, 42 items, optimum score: 100) in adults with haemophilia A/B. Data were divided into a derivation (62%) and a validation set (38%). Redundant items were identified by evaluation of: floor and ceiling effects, proportions of missing and 'not applicable' responses, inter-item correlations, component loadings in an exploratory factor analysis, internal consistency, and item-total correlations. Correlations with the SF-36 and EQ-5D-5L were used to determine construct validity of the HAL<sub>short</sub> .<h4>Results</h4>Data on 680 PWH were evaluated. In the derivation dataset (n = 420), median age was 30 years (range 18-80), 43% had severe haemophilia and 61% received prophylaxis. Median (IQR) HAL sum score was 65.0 (55.7-88.8). The stepwise procedure resulted in a HAL<sub>short</sub> of 18 items with a median sum score of 63.3 (54.4-86.7). Construct validity was similar for the HAL and HAL<sub>short</sub> in the validation dataset (n = 260).<h4>Conclusion</h4>This clinimetric study resulted in a >50% shortening of the HAL. The 18-item HAL<sub>short</sub> reduces patient burden and is expected to capture the information on activities and participation. The HAL<sub>short</sub> needs further validation.
Project description:BACKGROUND: Microbial oxidative degradation is a potential way of removing pollutants such as heterocycles from the environment. During this process, reactive oxygen species or other oxidants are inevitably produced, and may cause damage to DNA, proteins, and membranes, thereby decreasing the degradation rate. Carotenoids can serve as membrane-integrated antioxidants, protecting cells from oxidative stress. FINDINGS: Several genes involved in the carotenoid biosynthetic pathway were cloned and characterized from a carbazole-degrading bacterium Sphingobium yanoikuyae XLDN2-5. In addition, a yellow-pigmented carotenoid synthesized by strain XLDN2-5 was identified as zeaxanthin that was synthesized from ?-carotene through ?-cryptoxanthin. The amounts of zeaxanthin and hydrogen peroxide produced were significantly and simultaneously enhanced during the biodegradation of heterocycles (carbazole < carbazole + benzothiophene < carbazole + dibenzothiophene). These higher production levels were consistent with the transcriptional increase of the gene encoding phytoene desaturase, one of the key enzymes for carotenoid biosynthesis. CONCLUSIONS/SIGNIFICANCE: Sphingobium yanoikuyae XLDN2-5 can enhance the synthesis of zeaxanthin, one of the carotenoids, which may modulate membrane fluidity and defense against intracellular oxidative stress. To our knowledge, this is the first report on the positive role of carotenoids in the biodegradation of heterocycles, while elucidating the carotenoid biosynthetic pathway in the Sphingobium genus.
Project description:Among sphingomonads, Sphingobium indicum B90A is widely investigated for its ability to degrade a manmade pesticide, ?-hexachlorocyclohexane (?-HCH) and its isomers (?-, ?-, ?-, and ?-HCH). In this study, complete genome of strain B90A was constructed using Single Molecule Real Time Sequencing (SMRT) and Illumina platform. The complete genome revealed that strain B90A harbors four replicons: one chromosome (3,654,322?bp) and three plasmids designated as pSRL1 (139,218?bp), pSRL2 (108,430?bp) and pSRL3 (43,761?bp). The study determined the precise location of lin genes (genes associated with the degradation of HCH isomers), for example, linA2, linB, linDER, linF, linGHIJ, and linKLMN on the chromosome; linA1, linC, and linF on pSRL1 and linDEbR on pSRL3. Strain B90A contained 26 copies of IS6100 element and most of them (15 copies) was found to be associated with lin genes. Duplication of several lin genes including linA, linDER, linGHIJ, and linF along with two variants of linE, that is, linEa (hydroquinone 1,2-dioxygenase) and linEb (chlorohydroquinone/hydroquinone 1,2-dioxygenase) were identified. This suggests that strain B90A not only possess efficient machinery for upper and lower HCH degradation pathways but it can also act on both hydroquinone and chlorohydroquinone metabolites produced during ?-HCH degradation. Synteny analysis revealed the duplication and transposition of linA gene (HCH dehydrochlorinase) between the chromosome and pSRL1, possibly through homologous recombination between adjacent IS6100 elements. Further, in silico analysis and laboratory experiments revealed that incomplete tyrosine metabolism was responsible for the production of extracellular brown pigment which distinguished strain B90A from other HCH degrading sphingomonads. The precise localization of lin genes, and transposable elements (IS6100) on different replicons now opens up several experimental avenues to elucidate the functions and regulatory mechanism of lin genes acquisition and transfer that were not completely known among the bacterial population inhabiting the HCH contaminated environment.
Project description:A bacterium capable of utilizing dimethyl phthalate (DMP), diethyl phthalate (DEP), di-<i>n</i>-butyl phthalate (DBP), and diisobuthyl phthalate (DIBP) as the sole carbon and energy source was isolated from shallow aquifer sediments. The strain was identified as <i>Sphingobium yanoikuyae</i> SHJ based on morphological characteristics, 16S rDNA gene phylogeny, and whole genome average nucleotide identity (ANI). The degradation half-life of DBP with substrate concentration of 8.5 and 50.0 mg/L by strain SHJ was 99.7 and 101.4 hours, respectively. The optimum degradation rate of DBP by SHJ was observed at 30°C and weak alkaline (pH 7.5). Genome sequence of the strain SHJ showed a circular chromosome and additional two circular plasmids with whole genome size of 5,669,383 bp and GC content of 64.23%. Functional annotation of SHJ revealed a total of 5,402 genes, with 5,183 protein-encoding genes, 143 pseudogenes, and 76 noncoding RNA genes. Based on genome annotation, 44 genes were identified to be involved in PAEs hydrolysis potentially. Besides, a region with size of about 6.9 kb comprised of seven ORFs, which is located on the smaller plasmid pSES189, was presumed to be responsible for the biodegradation of phthalate. These results provide insights into the genetic basis of DBP biodegradation in this strain.
Project description:<b>Background:</b> The exoskeleton HAL (hybrid assistive limb) has proven to improve walking functions in spinal cord injury and chronic stroke patients when using it for body-weight supported treadmill training (BWSTT). Compared with other robotic devices, it offers the possibility to initiate movements actively. Previous studies on stroke patients did not compare HAL-BWSTT with conventional physiotherapy (CPT). Therefore, we performed a crossover clinical trial comparing CPT and HAL-BWSTT in chronic stroke patients with hemiparesis, the HALESTRO study. Our hypothesis was that HAL-training would have greater effects on walking and posture functions compared to a mixed-approach CPT. <b>Methods:</b> A total of 18 chronic stroke patients participated in this study. Treatment consisted of 30 CPT sessions and of 30 sessions of BWSTT with a double leg type HAL exoskeleton successively in a randomized, crossover study design. Primary outcome parameters were walking time and speed in 10-meter walk test (10MWT), time in timed-up-and-go test (TUG) and distance in 6-min walk test (6MWT). Secondary outcome parameters were the functional ambulatory categories (FAC) and the Berg-Balance Scale (BBS). Data were assessed at baseline, at crossover and at the end of the study, all without using and wearing HAL. <b>Results:</b> Our study demonstrate neither a significant difference in walking parameters nor in functional and balance parameters. When HAL-BWSTT was applied to naïve patients, it led to an improvement in walking parameters and in balance abilities. Pooling all data, we could show a significant effect in 10MWT, 6MWT, FAC and BBS, both therapies sequentially applied over 12 weeks. Thereby, FAC improve from dependent to independent category (3 to 4). One patient dropped out of the study due to intensive fatigue after each training session. <b>Conclusion:</b> HAL-BWSTT and mixed-approach CPT were effective therapies in chronic stroke patients. However, compared with CPT, HAL training with 30 sessions over 6 weeks was not more effective. The combination of both therapies led to an improvement of walking and balance functions. Robotic rehabilitation of walking disorders alone still lacks the proof of superiority in chronic stroke. Robotic treatment therapies and classical CPT rehabilitation concepts should be applied in an individualized therapy program.
Project description:Sphingobium sp. strain SYK-6 is able to grow on an extensive variety of lignin-derived biaryls and monoaryls, and the catabolic genes for these compounds are useful for the production of industrially valuable metabolites from lignin. Here we report the complete nucleotide sequence of the SYK-6 genome which consists of the 4,199,332-bp-long chromosome and the 148,801-bp-long plasmid.
Project description:<h4>Motivation</h4>Large multiple genome alignments and inferred ancestral genomes are ideal resources for comparative studies of molecular evolution, and advances in sequencing and computing technology are making them increasingly obtainable. These structures can provide a rich understanding of the genetic relationships between all subsets of species they contain. Current formats for storing genomic alignments, such as XMFA and MAF, are all indexed or ordered using a single reference genome, however, which limits the information that can be queried with respect to other species and clades. This loss of information grows with the number of species under comparison, as well as their phylogenetic distance.<h4>Results</h4>We present HAL, a compressed, graph-based hierarchical alignment format for storing multiple genome alignments and ancestral reconstructions. HAL graphs are indexed on all genomes they contain. Furthermore, they are organized phylogenetically, which allows for modular and parallel access to arbitrary subclades without fragmentation because of rearrangements that have occurred in other lineages. HAL graphs can be created or read with a comprehensive C++ API. A set of tools is also provided to perform basic operations, such as importing and exporting data, identifying mutations and coordinate mapping (liftover).<h4>Availability</h4>All documentation and source code for the HAL API and tools are freely available at http://github.com/glennhickey/hal.<h4>Contact</h4>firstname.lastname@example.org or email@example.com<h4>Supplementary information</h4>Supplementary data are available at Bioinformatics online.
Project description:<i>Sphingobium barthaii</i> KK22<sup>T</sup> is a high-molecular-weight polycyclic aromatic hydrocarbon-degrading soil bacterium that has been investigated in biotransformation, microbial ecology, and DNA damage studies. The complete genome sequence of <i>S. barthaii</i> revealed four closed circular sequences, including two chromosomes, a megaplasmid, and a smaller plasmid, by hybrid assembly using short- and long-read sequencing technologies.
Project description:The Hybrid Assistive Limb (HAL®) is an exoskeleton wearable robot suit that assists in voluntary control of knee and hip joint motion. There have been several studies on HAL intervention effects in stroke, spinal cord injury, and cerebral palsy. However, no study has investigated HAL intervention for patients with cerebral palsy after surgery.We report a case of using HAL in a postoperative patient with cerebral palsy. A 15-year-old boy was diagnosed with spastic diplegia cerebral palsy Gross Motor Function Classification System level IV, with knee flection contracture, equinus foot, and paralysis of the right upper extremity with adduction contracture. He underwent tendon lengthening of the bilateral hamstrings and Achilles tendons. Although the flexion contractures of the bilateral knees and equinus foot improved, muscle strength decreased after the soft tissue surgery. HAL intervention was performed twice during postoperative months 10 and 11. Walking speed, stride, and cadence were increased after HAL intervention. Post HAL intervention, extension angles of the knee in stance phase and hip in the pre-swing phase were improved. In the gait cycle, the proportion of terminal stance in the stance and swing phase was increased.Hybrid Assistive Limb intervention for postoperative patients with cerebral palsy whose muscle strength decreases can enhance improvement in walking ability. Further studies are needed to examine the safety and potential application of HAL in this setting.